Filter Counts
Keep transcripts with at least 2 samples that have >= 10
counts
Covariate Data for DESeq2
Run DESeq2
estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
Add Gene Names to Differential Expression Results
Rows: 385669 Columns: 8
── Column specification ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: "\t"
chr (6): transcript_id, gene_id, gene_symbol, gene_version, chr, strand
dbl (2): start, end
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
PCA on vst Normalized Counts
using ntop=500 top features by variance

using ntop=500 top features by variance

using ntop=500 top features by variance


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